#TEMPORARY ACCESSION NUMBER:


#ACCESSION NUMBER:

#CONTRIBUTOR:
        Charles A. Si Simenstad
        Fisheries Research Institute
        University of Washington
        Box 357980
        Seattle, WA  98195-7980  USA
        email: csimenstad@lternet.edu


#CONTRIBUTOR INSTITUTION:
        Fisheries Research Institute
        University of Washington
        Box 357980
        Seattle, WA  98195-7980  USA
        email: csimenstad@lternet.edu

#ORIGINATOR:
same

#ORIGINATOR INSTITUTION:
same

#TITLE:
Involves scientists from six distinct disciplines-geophysics, sedimentology, geochemistry,
microbiology, primary production biology, and zooplankton and food web ecology-to characterize 
estuarine turbidity maximum process in the Lower Columbia River estuary.  Our research site is in the Columbia River estuary, at the
coastal border of Washington and Oregon states (USA), but both our measurements and our interest stretch upriver into the
watershed.



#PROJECT:
The Columbia River Estuarine Turbidity Maximum (CRETM) research program


#ABSTRACT:
Although the Columbia River is distinct among the LMER sites around the country, it represents a distinct class of systems
(river estuaries typified by estuarine turbidity maxima) of great importance throughout the world (ETMs around the world).
The Columbia River and its estuary exemplify some of the many ways that man has modified the structure of land-margin
ecosystems and the fundamental processes that sustain them. Despite the large size of the Columbia River and its watershed,
upriver impoundments behind dams, land and water use, and diking, filling and dredging in the lower river and estuary have
substantially altered the river system (see Nch'i-Wana). This manipulation of the river has changed patterns and magnitude of
flow, greatly reduced the load of sediments carried to the estuary by the river, changed the river's chemistry, and altered the
various ETM processes that transform organic matter into the estuary's food web. While the estuary and lower river are
certainly not free of pollution effects (especially pesticide residues in higher trophic level organisms), it is still relatively free of
any indications of eutrophication and hypoxia that have plagued other large estuaries.



#PURPOSE:
Our fundamental research goal is to understand how circulation phenomena in the estuary, called estuarine turbidity maxima
(ETM), trap particles and promote biogeochemical, microbial and ecological processes that sustain a dominant pathway in the
estuary's food web. To study this relationship between the physics of ETM and these various processes requires a resolutely
interdisciplinary approach, and a complex, highly-orchestrated suite of field and laboratory measurements and experiments.
The CRETM-LMER team involves scientists from six distinct disciplines-geophysics, sedimentology, geochemistry,
microbiology, primary production biology, and zooplankton and food web ecology-to characterize ETM process. But, we
depend upon hydrodynamic and ecosystem process modelers to help us synthesize our understanding about how the ETM
and associated estuarine processes act as a "living" system that is fundamental to the way the estuary behaves.



#LOCATION EXTREMES:
SOUTHERNMOST LATITUDE: 45 30'   HEMISPHERE: N
NORTHERNMOST LATITUDE: 46 30'   HEMISPHERE: N  
WESTERNMOST LONGITUDE: 124 00'  HEMISPHERE: W 
EASTERNMOST LONGITUDE: 122 00'  HEMISPHERE: W




#LOCATION KEYWORDS:
Pacific Ocean, Columbia River, Lower Columbia River
 
 57E, 57J


#SAMPLING STATIONS:
Sampling stations are too numerous to list on this form, for station information, refer
to the CRETM/LMER web site under station and related metadata.
(http://depts.washington.edu/cretmweb/datamenu.html)

A little basic information is provided immediately below.

Because ETM move with the tides and vary in location with the river
flow and the estuary's bathymetry, we sample at a number of stations within the range of ETM, as well as above and below it.
Many of our sampling locations within the ETM zone are near Astoria, OR, or about 23 km (14 miles) from the river mouth.
Another station is 85 km (53 miles) above the mouth of the estuary (Beaver Terminal), well beyond the intrusion of seawater,
where we assess the composition and amount of particulate matter that the river is delivering to the estuary. We have also
conducted sampling even further upriver (above the lowest two dams) to sample variability in inputs from different tributaries
and sub-basins of the watershed.



#BEGIN AND END DATES:
BEGIN DATE: 1997/05/03
END DATE: 1998/03/04

#SAMPLING PERIODS:
1997/05/03 - 1997/05/15

1997/07/07 - 1997/07/19

1997/10/16 - 1997/10/19

1998/02/21 - 1998/03/04


#PARAMETERS:
        Code            cast-specific code number (see below)
        Date            date in MM/DD/YY format
        Time            time of day (Pacific standard time)
        Depth           depth in meters
        OBS             optical backscattering (see below) 
                Densities:              ( # / m3)
        PICOPE          Pseudodiaptomus inopinus (copepodite)
        PIMALE          P. inopinus (male)
        PINOFEM         P. inopinus (non-ovigerous female)
        PIOVIF          P. inopinus (ovigerous female)
        PIADULT         P. inopinus (total adults)
        PITOT           P. inopinus (total)
        EA1-3           Eurytemora affinis (copepodite 1-3)
        EA4-5           E. affinis (copepodite 4-5)
        EAMALE          E. affinis (male)
        EANOFEM         E. affinis (non-ovigerous female)
        EAOVIF          E. affinis (ovigerous female)
        EAADULT         E. affinis (total adults)
        EATOT           E. affinis (total)
        CC1-5           Coullana (= Scottolana) canadensis (copepodite 1-5)
        CCMALE          C. canadensis (male)
        CCNOFEM         C. canadensis (non-ovigerous female)
        CCOVIF          C. canadensis (ovigerous female)
        CCMATE          C. canadensis (mating pairs)
        CCADULT         C. canadensis (total adults)
        CCTOT           C. canadensis (total)
        BOSMINA         Bosmina longirostris (all stages)
        PSBRADYA        Pseudobradya sp. (total)
        AVADULT         Acanthocyclops vernalis (adult)
        AVCOP           A. vernalis (copepodite)
        DTADULT         Diacyclops thomasi (adult)
        DTCOP           D. thomasi (copepodite) 
        ROTIFER         rotifers
        COPNAUP         calanoid copepod nauplii
        CYCLCOP         cyclopoid copepod copepodites   
        OTHER           other taxa
        TotZoop         total zooplankton density (#/m3)



#METHODOLOGY:
Pump casts were conducted immediately following a CTD cast and are, thus, cross-referenced by CTD data parameters.  A volume of 20 L was 
collected, sieved through a 200 um sieve on deck, and fixed with formalin  In the lab, preserved zooplankton were indentified, staged, and counted under 
stereomicroscopes.  Details of methodology are referenced in Cordell et al. (1992) and Simenstad et al. (1994). 
        


#INSTRUMENT TYPES:
Measurements were conducted from an anchored vessel.  A Seabird (1990-1992) SBE 9/11 or Ocean 
Sensors (1995-1996) model OS-200 CTD equipped with a CT cell, OBS sensor, and a WetLabs AC-3 chlorophyll 
absorption-attenuation sensor were deployed for vertical profiles approximately every 30 minutes.  More frequent 
casts were conducted during "high intensity" sampling (e.g E or F series, see below).  Data were averaged into 
0.2 m bins and referenced from the surface (i.e. not de-tided).



#REFERENCES:
Annotated Bibliography of CRETM-LMER Publications

 

 

1992

Cordell, J. R., C. A. Simenstad, and C. A. Morgan. 1992. Occurrence of the Asian calanoid copepod Pseudodiaptomus
inopinus in the Columbia River estuary. J. Crustacean Biol. 12:260-269. Abstract

Cordell, J. R., C. A. Simenstad, and C. A. Morgan. 1992. The Asian calanoid copepod Pseudodiaptomus inopinus in
Pacific Northwest rivers--biology of an invasive zooplankter. N.W. Environ. J. 8:164-165.

LMER Coordinating Committee (Boynton, W., J. T. Hollibaugh, D. Jay, M. Kemp, J. Kremer, C. Simenstad, S. V. Smith,
and I. Valiela). 1992. Understanding changes in coastal environments: the Land Margin Ecosystems Research Program. EOS
73: 481-485.

Morgan, S. R. 1992. Seasonal and tidal influence of the estuarine turbidity maximum on primary biomass and production in the
Columbia River estuary. M.S. thesis, Oregon State Univ., Corvallis, OR. 87pp. Abstract

Prahl F. G., Hayes J. M. and Xie T. -M. 1992. Diploptene, an indicator of soil organic matter in Washington coastal
sediments. Limnol. Oceanogr. 37: 1290-1300. Abstract

Simenstad, C. A., D. A. Jay and C. R. Sherwood. 1992. Impacts of watershed management on land-margin ecosystems: The
Columbia River estuary as a case study. Pp. 266-306 In R. J. Naiman (ed.), New Perspective in Watershed Management,
Springer-Verlag, New York. 543 pp. Abstract

 

1993

Morgan, C. A. 1993. Sink or swim? Copepod population maintenance in the Columbia River estuarine turbidity maxima
region. M.S. thesis, Univ. Washington, Seattle, WA. 85 pp. Abstract

 

1994

Baross, J. A., B. Crump, and C. A. Simenstad. 1994. Elevated 'microbial loop' activities in the Columbia River estuary
turbidity maximum. Pp. 459-464 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from
Science to Management, ECSAERF22 Symposium, Olsen & Olsen Press, Friedensborg. Abstract

Jay, D. A. 1994. Residence time, box models and shear fluxes in tidal channel flows. Pp. 3-12 In K. Dyer and R. Orth (ed.),
Changing Particle Fluxes in Estuaries: Implications from Science to Management, ECSAERF22 Symposium, Olsen &
Olsen Press, Friedensborg. Abstract

Jay, D. A. and J. D. Musiak. 1994. Particle trapping in estuarine turbidity maxima. J. Geophys. Res. 99: 20,446-461.
Abstract

Keil R.G., E. Tsamakis, C. B. Fuh, J. C. Giddings and J. I. Hedges J.I. 1994. Mineralogical and textural controls on the
organic composition of coastal marine sediments: hydrodynamic separations using SPLITT-fractionation. Geochim.
Cosmochim. Acta 58: 879-893. Abstract

Prahl F. G. and Coble P. G. 1994. Input and behavior of dissolved organic carbon in the Columbia River Estuary. Pp.
451-457 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to
Management, ECSAERF22 Symposium, Olsen & Olsen Press, Friedensborg. Abstract

Prahl, F. G., J. R. Ertel, M. A. Goni, M. A. Sparrow and B. Eversmeyer. 1994. Terrestrial organic carbon contributions to
sediments on the Washington margin. Geochim. Cosmochim. Acta 58: 3035-3048. Abstract

Reed, D. J. and J. Donovan. 1994. The character and composition of the Columbia River estuarine turbidity maximum. Pp.
445-450 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to
Management, ECSAERF22 Symposium, Olsen & Olsen Press, Friedensborg. Abstract

Simenstad, C. A., D. J. Reed, D. A. Jay, J. A. Baross, F. G. Prahl and L. F. Small. 1994a. Land-margin ecosystem research
in the Columbia River estuary: investigations of the couplings between physical and ecological processes within estuarine
turbidity maxima. Pp. 437-444 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from
Science to Management, ECSAERF22 Symposium, Olsen & Olsen Press, Friedensborg. Abstract

Simenstad, C. A., C. A. Morgan, J. R. Cordell, and J. A. Baross. 1994b. Flux, passive retention, and active residence of
zooplankton in Columbia River estuarine turbidity maxima. Pp. 473-482 In K. Dyer and R. Orth (ed.), Changing Particle
Fluxes in Estuaries: Implications from Science to Management, ECSAERF22 Symposium, Olsen & Olsen Press,
Friedensborg. Abstract

Small, L. F., and S. R. Morgan. 1994. Phytoplankton attributes in the turbidity maximum of the Columbia River Estuary,
USA. Pp. 465-472 In K. Dyer and R. Orth (ed.), Changing Particle Fluxes in Estuaries: Implications from Science to
Management, ECSAERF22 Symposium, Olsen & Olsen Press, Friedensborg. Abstract

 

1995

Jay, D. A., and E. P. Flinchem. 1995. Wavelet transform analyses of non-stationary tidal currents. Pp. 101-106 In S.
Anderson, J. R. Appel, and A. E. Willimas (eds.), Proc. IEEE Fifth Working Conf. Current Measurement.

Jay, D. A. and J. D. Musiak. 1995. Internal Tidal Asymmetry in Channel Flows: Origins and Consequences. Pp. 219-258 In
C. Pattiaratchi (ed.), Mixing Processes in Estuaries and Coastal Seas, Amer. Geophy. Union, Coastal Estuar. Sci.
Monogr. Abstract

 

1996

Cordell, J. R., and S. M. Morrison. 1996. The invasive Asian copepod Pseudodiaptomus inopinus in Oregon, Washington,
and British Columbia estuaries. Estuaries 19: 629-638. Abstract

Crump, B., and J. A. Baross. 1996. Particle-attached bacteria and heterotrophic plankton associated with the Columbia River
estuarine turbidity maxima. Mar. Ecol. Prog. Ser. 138: 265-273. Abstract

Cudaback, C. N. and D. A. Jay. 1996. Formation of the Columbia River plume: hydraulic control in action? In D. G. Aubrey
(ed.), Buoyany Effects on Coastal Dynamics, AGU Coastal Est. Sci. Monogr. 53: 139-154.Abstract

Fortunato, A. B., and A. M. Baptista. 1996. Vertical discretization in tidal flow simulations. Internat. J. Numerical Methods
Fluids 22:815-834. Abstract

Fortunato, A. B., and A. M. Baptista. 1996. Evaluation of horizontal gradients in sigma-coordinate shallow water model.
Atmosphere-Ocean 34: 489-514. Abstract

Jay, D. A. and C. A. Simenstad. 1996. Downstream Effects of Water Withdrawal in a Small, High-Gradient Basin: Erosion
and Deposition on the Skokomish River Delta. Estuaries 19: 501-517. Abstract

Kay, D. J., D. A. Jay and J. D. Musiak, 1996. Salt transport through an estuarine cross-section calculated from moving vessel
ADCP and CTD data. In D. G. Aubrey (ed.), Buoyancy Effects on Coastal and Estuarine Dynamics, AGU Coastal and
Estuarine Studies 53:195-212. Abstract

1997

Jay, D. A., and E. P. Flinchem. 1997. Interaction of fluctuating river flow with a barotrophic tide: a demonstration of wavelet
tidal analysis methods. J. Geophys. Res. 102:5705-5720. Abstract

Jay, D. A., R. J. Uncles, J. Largier, W. R. Geyer, J. Vallino, W. R. Boynton, 1997. Recent developments in estuarine scalar
flux estimation. Estuaries 20: 262-280. Abstract

Morgan, C. A., J. R. Cordell, and C. A. Simenstad. 1997. Sink or swim? Copepod population maintenance in the Columbia
River estuarine turbidity maxima region. Mar. Biol. 129:309-317. Abstract

Oliveira, A., and A. M. Baptista. 1997. Diagnostic modeling of residence times in estuaries. Wat. Resources Res.
33:1935-1946. Abstract

Prahl, F. G., L. F. Small, and B. Eversmeyer. 1997. Biogeochemical characterization of suspended particulate matter in the
Columbia River estuary. Mar. Ecol. Prog. Ser. 160:173-184. Abstract

Simenstad, C. A., M. Dethier, C. Levings, and D. Hay. 1997. The Land- Margin Interface of Coastal Temperate Rain Forest
Ecosytems: Shaping the Nature of Coastal Interactions. Pp. 149-187 (Chap. 7) in P. Schoonmaker, B. von Hagen, and E.
Wolf (eds.) The Rain Forests of Home: Profile of a North American Bioregion. Ecotrust/Interain Pacific and Island
Press. 480 pp.

Sullivan, B. E., 1997. Annual cycles of organic matter and phytoplankton attributes in the Columbia and Willamette Rivers,
with reference to the Columbia River estuary. M.S. thesis, Oregon State University, Corvallis, OR. 114 pp.

 

1998

Crump, B. C., J. A. Baross and C. A. Simenstad. 1997. Dominance of particle-attached bacteria in the Columbia River
estuary. Aquat. Microb. Ecol. 14:7-18. Abstract

Cudaback, C. N., 1998. The effect of vertical mixing on along-channel transport in a layered flow. Ph.D. dissertation,
University of Washington, Seattle, WA Abstract

Prahl, F. G., L. F. Small, B. A. Sullivan, J. Cordell, C. A. Simenstad, B. C. Crump and J. A. Baross. 1998. Biogeochemical
gradients in the lower Columbia River. Hydrobiologia 361:37-52. Abstract

 

1999

Crump, B.C. E.V. Armbrust, and J.A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial
communities in the Columbia River, estuary, and adjacent coastal ocean. Applied and Environmental Microbiology 65(7):
3192-3204. Abstract

Jay, D.A., P. Orton, D.J. Kay, A. Fain and A.M. Baptista. 1999. Acoustic determination of sediment concentrations, settling
velocities, horizontal transports and vertical fluxes in estuaries. Proceedings of the IEEE Sixth Working Conference on
Current Measurement, S. P. Anderson, E. A. Terray, J. A. Rizzoli White, and A. J. Williams, III, eds. 258-263. Abstract

Jay, D.A. and E.P. Flinchem. 1999. A comparison of methods for analysis of tidal records containing multi-scale non-tidal
background energy. Continental Shelf Research. Abstract

 

2000

Crump B.C. and J.A. Baross. 2000. Archaeaplankton in the Columbia River, its estuary, and the adjacent coastal ocean,
USA. FEMS Microbiol Ecol. 1104:1-9.

 

Submitted and In press

Baptista, A. M., M. Wilken, P. Pearson, C. McCandlish, D. Jay, B. Beck, S. Das, J. Hunt, P. Barrett. Towards a
Nowcast-Forecast System for the Columbia River Estuary. Proceedings of the 5th International Conference on Estuarine
and Coastal Modeling, Alexandria, VA (in press) Abstract

Cudaback, C. N. and D. A. Jay. Lateral force balance and circulation processes at the mouth of the Columbia River estuary.
Submitted to Estuarine, Coastal and Shelf Sci.

Cudaback, C. N., and D. A. Jay. 1999. Vertical Mixing and Estuarine Exchange Transport: I. Observations and a Two-Layer
Analysis. Submitted to J. Geophys. Res.

Cudaback, C. N., and D. A. Jay. 1999. Vertical Mixing and Estuarine Exchange Transport: II. A Three-Layer Model.
Submitted to J. Geophys. Res. 

Flinchem, E. P. and D. A. Jay. 2000. An introduction to wavelet transform tidal analysis methods. In Press. Coast. Estuar.
Shelf Sci. Abstract 

Geyer, W. R., J. T. Morris, F. G. Prahl and D. A. Jay, and. E. Turner. 1999. The coupling of physics, biogeochemistry and
ecology. In Press. Estuarine Science, A Synthetic Approach to Research and Practice, J. E. Hobbie, ed. Island Press. 

Jay, D. A., W. R. Geyer and D. R. Montgomery. 1999. An ecological perspective on estuarine classification. In press.
Estuarine Science, A Synthetic Approach to Research and Practice, J. E. Hobbie (ed.), Island Press. Abstract

Kay, D. J. and D. A. Jay. 1999. Interfacial mixing in a highly-stratified estuary. 1: Characteristics of Mixing. Submitted to J.
Geophys. Res.

Kay, D. J. and D. A. Jay. 1999. Interfacial mixing in a highly-stratified estuary. 2. a "method of constrained differences"
approach for the determination of the momentum and mass balances and the energy of mixing. Submitted to J. Geophys. Res. 

Sullivan, B.E., F.G. Prahl, L.F. Small and P.A. Covert. Seasonal variations in suspended particle and freshwater
phytoplankton input to the Columbia River estuary.



#SUBMITTING MEDIUM:
ftp

#FILE FORMATS:
        File format: comma-delineated ASCII with header;


        Code            cast-specific code number (see below)
        Date            date in MM/DD/YY format
        Time            time of day (Pacific standard time)
        Depth           depth in meters
        OBS             optical backscattering (see below) 
        Densities:              ( # / m3)
        PICOPE          Pseudodiaptomus inopinus (copepodite)
        PIMALE          P. inopinus (male)
        PINOFEM         P. inopinus (non-ovigerous female)
        PIOVIF          P. inopinus (ovigerous female)
        PIADULT         P. inopinus (total adults)
        PITOT           P. inopinus (total)
        EA1-3           Eurytemora affinis (copepodite 1-3)
        EA4-5           E. affinis (copepodite 4-5)
        EAMALE          E. affinis (male)
        EANOFEM         E. affinis (non-ovigerous female)
        EAOVIF          E. affinis (ovigerous female)
        EAADULT         E. affinis (total adults)
        EATOT           E. affinis (total)
        CC1-5           Coullana (= Scottolana) canadensis (copepodite 1-5)
        CCMALE          C. canadensis (male)
        CCNOFEM         C. canadensis (non-ovigerous female)
        CCOVIF          C. canadensis (ovigerous female)
        CCMATE          C. canadensis (mating pairs)
        CCADULT         C. canadensis (total adults)
        CCTOT           C. canadensis (total)
        BOSMINA         Bosmina longirostris (all stages)
        PSBRADYA        Pseudobradya sp. (total)
        AVADULT         Acanthocyclops vernalis (adult)
        AVCOP           A. vernalis (copepodite)
        DTADULT         Diacyclops thomasi (adult)
        DTCOP           D. thomasi (copepodite) 
        ROTIFER         rotifers
        COPNAUP         calanoid copepod nauplii
        CYCLCOP         cyclopoid copepod copepodites   
        OTHER           other taxa
        TotZoop         total zooplankton density (#/m3)

Explanation of Code:
        Format of code is:  YYBSENN
                
                YY      first two digits indicate year
                B       letter(s) indicates boundary location or tidal series as follows: U=upstream (beyond salt wedge), D=downstream (below 
estuarine turbidity maximum), N=neap tide, S=spring tide, SN=spring-neap transition, E= ebb, F=flood, L=long time series, YB=Youngs Bay, 
CB=Cathlamet Bay
                S       number of sample series at that location/tidal stage
                E       event number (sequence) within that series (an E or F may follow this number indicating and ebb or flood tide sampling
                NN      two (or three) digits indicate CTD cast number that corresponds to the pump cast
                *       an asterisk after the code indicates CTD data taken from the downcast immediately prior to the pump cast

Other data notes:

        *** OBS units are linearly related to suspended particulate material as measured in mg/L.

        maximum number of records = ###;
        maximum record length = ###


#FILENAMES:
1) 97azoop.txt
2) 97bzoop.txt
3) 97czoop.txt
4) 98azoop.txt


#DATASET SIZE:
82 kb


#MISCELLANEOUS:
(for station information, refer to CRETM/LMER web site, station info too
extensive for this form - see web site reference under station information)
Information also available via files submitted to the NODC.
Ref.;
mark97a.txt
mark97b.txt
mark97c.txt
mark98a.txt


